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Series GSE39780 Query DataSets for GSE39780
Status Public on Aug 10, 2013
Title Zygotic gene activatory network in zebrafish is globally controlled by Pou5f1 SoxB1 enhancers
Organism Danio rerio
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genetic control of pluripotent mammalian ES cells is determined by a transcriptional network, with a "central core" of transcription factors, Pou5f1, Sox2 and Nanog. Zebrafish homologues of the "core pluripotency factors" Pou5f1, SoxB1 and Nanog-like are also crucially involved in early development. However, the degree of functional similarity of the network between mammals and non-mammals is a matter of debate. To identify the components of Pou5f1-dependent transcriptional networks, we determined the genomic binding sites for Pou5f1 and Sox2 in late blastula stage zebrafish embryos using ChIP-seq. We found that Sox2 and Pou5f1 are co-binding to the regulatory regions of Sox2, Pou5f1, and Nanog-like, as well as to multiple orthologues of mammalian plutipotency network components.
Overall design Deep sequencing was performed using the Illumina GAIIx on DNA samples obtained from Sox2 ChIP, Pou5f1-Flag ChIP and Input Control. Pou5f1 was analysed in technical duplicates to obtain higher sequencing depth.
Contributor(s) Leichsenring M, Maes J, Mössner R, Driever W, Onichtchouk D
Citation(s) 23950494
Submission date Jul 31, 2012
Last update date May 15, 2019
Contact name Manuel Leichsenring
Organization name Albert-Ludwigs-University Freiburg
Street address Hauptstr. 1
City Freiburg
ZIP/Postal code 79104
Country Germany
Platforms (2)
GPL14875 Illumina HiSeq 2000 (Danio rerio)
GPL15583 Illumina Genome Analyzer IIx (Danio rerio)
Samples (4)
GSM978984 Sox2 ChIP
GSM978985 Pou5f1-Flag ChIP
GSM978986 Input DNA
BioProject PRJNA171706
SRA SRP014632

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE39780_RAW.tar 760.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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